Designing and Analyzing the Structure of DT-STXB Fusion Protein as an Anti-tumor Agent: An in Silico Approach

Abstract

Background & objective: A main contest in chemotherapy is to obtain regulator above the biodistribution of cytotoxic drugs. The utmost promising strategy comprises of drugs coupled with a tumor-targeting bearer that results in wide cytotoxic activity and particular delivery. The B-subunit of Shiga toxin (STxB) is nontoxic and possesses low immunogenicity that exactly binds to the globotriaosylceramide (Gb3/CD77). Gb3/CD77 extremely expresses on a number of human tumors such as pancreatic, colon, and breast cancer and acts as a functional receptor for Shiga toxin (STx). Then, this toxin can be applied to target Gb3-positive human tumors. In this study, we evaluated DT390-STXB chimeric protein as a new anti-tumor candidate via genetically fusing the DT390 fragment of DT538 (Native diphtheria toxin) to STxB.

Methods: This study intended to investigate the DT390- STxB fusion protein structure in silico. Considering the Escherichia coli codon usage, the genomic construct was designed. The properties and the structure of the protein were determined by an in silico technique. The mRNA structure and the physicochemical characteristics, construction, and the stability of the designed chimeric protein were analyzed using computational and bioinformatics tools and servers. Hence, the GOR4 and I-TASSER online web servers were used to predict the secondary and tertiary structures of the designed protein.

Results: The results demonstrated that codon adaptation index (CAI) of dt390-stxB chimeric gene raised from 0.6 in the wild type to 0.9 in the chimeric optimized gene. The mfold data revealed that the dt390-stxB mRNA was completely stable to be translated effectively in the novel host. The normal activity of the fusion protein determined by considering the secondary and tertiary structure of each construct. Energy calculation data indicated that the thermodynamic ensemble for mRNA structure was -427.40 kJ/mol. The stability index (SI) of DT390-STxB was 36.95, which is quite appropriate to preserve the stability of the construct. Ultimately, the DT390-STxB was classified as a steady fusion protein according to the Ramachandran plot.

Conclusion: Our results showed that DT390-STXB was a stable chimeric protein and it can be recruited as a candidate of novel anti-tumor agents for the development of breast cancer treatment.

Keywords: Bioinformatics tools; Cancer therapy; Diphtheria toxin; In silico modeling; Shiga-like toxin part B.

Fig. 1

A. Sequence alignment and schematic model of hypothetical chimeric protein, which has exposed the construct of DT390 (catalytic and translocate domains) and STxB bound together by the GGGGSGGGGSGGGGS appropriate linker for expression in E. coli. B. Adaptation of codon usage intermittent repartition. The red line demonstrates the codon usage for every codon, which is present in the gene. The blue line shows the mean codon usage in E. coli which was assessed for any recognized gene of this organism. The grey lines above and under the blue line display the standard deviation for this mean codon usage in the E. coli. C. Graphical picture of secondary elements in chimeric DT390-STxB protein. The solubility supplies have been categorized by the main polarity and hydrophobic properties of residual patterns. These patterns have exposed that the mean residue accessible surface area (ASA) have given a high solvent convenience value

Fig. 2

The mRNA secondary structure of dt390-stxB prediction. Predicted structure has a pseudoknot at 5′ site of mRNA. (ΔG=-427.40 kJ/mol) in mfold tool

Figure 3

Tertiary structure prediction. A probabilistic structural model for DT390-STxB chimeric protein by ITASSER server. Based on C-scores, the model 1 has a high confidence score among other models

Figure 4

Evaluation of model stability is based on a Ramachandran plot for the DT390-STxB chimeric protein